Progress has been made in physically characterizing three distinct systems, all of which have possible biological significance. A substantial difference in the bending energy or flexibility has been found between poly (dG-dC) and its methylated analogue, poly (dG-m5dC). This difference makes it probable that resistance to bending is largely due to perturbations in groove hydration rather than in base stacking interactions. It also suggests that a biological effect of CpG methylation is to potentiate the ease of nucleosome formation relative to protein factor binding. We have identified the source of entropy, that drives the conformational transition from the B to Z forms of poly(dG-m5dC), as the release of two water molecules per base pair. This result suggests that this transition will be significantly easier in the cell, under conditions of osmotic stress, than in dilute solution. The conformational change that occurs with ATP binding to gyrase-DNA complexes has been determined. The DNA tails, that extend out from the core in the basic complex, fold back cross the protein when ATP is added. These results will enable us to correlate mechanism, biochemistry, and structure for the supercoiling reaction of gyrase.